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MRG, BUG: Fix vector scaling#7934

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agramfort merged 2 commits intomne-tools:masterfrom
larsoner:vector
Jun 27, 2020
Merged

MRG, BUG: Fix vector scaling#7934
agramfort merged 2 commits intomne-tools:masterfrom
larsoner:vector

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@larsoner larsoner commented Jun 25, 2020 •
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Fixes the bug with glyph colormap not being updated, tested with:

Details 
import os.path as op
import mne

data_path = mne.datasets.sample.data_path()
sample_dir = op.join(data_path, 'MEG', 'sample')
subjects_dir = op.join(data_path, 'subjects')
inv = mne.minimum_norm.read_inverse_operator(op.join(
    sample_dir, 'sample_audvis-meg-oct-6-meg-inv.fif'))
evoked = mne.read_evokeds(op.join(sample_dir, 'sample_audvis-ave.fif'))[0]
evoked.apply_baseline((None, 0))
stc = mne.minimum_norm.apply_inverse(
    evoked, inv, method='dSPM', verbose='debug', pick_ori='vector')  # 'vector')
initial_time = 0.1

size = (800, 400)
with mne.viz.use_3d_backend('pyvista'):
    brain = stc.plot(subjects_dir=subjects_dir, initial_time=initial_time,
                     clim='auto', views='lat', hemi='lh',
                     smoothing_steps='nearest', verbose=True,
                     size=size, background='k')

A few things along the way:

  1. Consolidate update_lut so that there is no longer a need for the very repeat-y update_fmin, update_fmid, and update_fmax
  2. Refactor some time viewer slider controls to make one call to update_lut instead of potentially multiple calls like update_fmin followed by update_fmid
  3. Make update_fscale private (I don't think it was meant to be public)
  4. Never apply alpha to the LUT, but instead apply it to the mesh(..., opacity=alpha) instead.

Approximately 3x minus-to-plus ratio on this PR suggesting that it's DRYing out our code. No test added because I'm not sure that there is a great way to test this. In theory if there were existing vector + TimeViewer tests it could be added there, but in a quick check I did not see any. @GuillaumeFavelier feel free to correct me if I'm wrong...

@GuillaumeFavelier GuillaumeFavelier mentioned this pull request Jun 25, 2020
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GuillaumeFavelier commented Jun 26, 2020 •
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here were existing vector + TimeViewer tests it could be added there, but in a quick check I did not see any

Its test is test_plot_vector_source_estimates in test_3d.py. The renderer_interactive fixture makes it available for the PyVista backend with time_viewer=True and show_traces='auto'.

@agramfort agramfort merged commit 31a82ec into mne-tools:master Jun 27, 2020
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agramfort commented Jun 27, 2020

thx @larsoner

@larsoner larsoner deleted the vector branch June 28, 2020 12:52
larsoner added a commit to larsoner/mne-python that referenced this pull request Jul 8, 2020
@larsoner
Merge remote-tracking branch 'upstream/master' into refactor
b60f9b0 
* upstream/master: (30 commits)
  MRG: Add remove_labels to _Brain (mne-tools#7964)
  Add get_picked_points (mne-tools#7963)
  ENH: Add OpenGL info to mne sys_info (mne-tools#7976)
  [MRG] Fix reject_tmin and reject_tmax for reject_by_annotation in mne.Epochs (mne-tools#7967)
  mrg: Add scalar mult and div operators for AverageTFR (mne-tools#7957)
  MRG, MAINT: Cleaner workaround for Sphinx linking issue (mne-tools#7970)
  MRG, ENH: Speed up epochs.copy (mne-tools#7968)
  MRG, BUG: Allow ref mags to have a comp grade (mne-tools#7965)
  do not forget to pass adjacency (mne-tools#7961)
  [MRG] fix Issue with stc.project after restricting to a label (mne-tools#7950)
  Only process nirx event file if present (mne-tools#7951)
  MRG+1: BUG: info['bads'] order shouldn't matter in write_evokeds() (mne-tools#7954)
  Fix some small glitches introduced via mne-tools#7845 (mne-tools#7952)
  Add time player (mne-tools#7940)
  MAINT: Clean up VTK9 offset array [circle front] (mne-tools#7953)
  MAINT: Skip a few more on macOS (mne-tools#7948)
  fix links [skip travis] (mne-tools#7949)
  MRG, MAINT: Tweak CIs (mne-tools#7943)
  MRG, BUG: Fix vector scaling (mne-tools#7934)
  MRG, VIZ, BUG: handle CSD channel type when topo plotting (mne-tools#7935)
  ...
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@larsoner @GuillaumeFavelier @agramfort